Starting phenix.real_space_refine on Mon Jun 9 21:13:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n7i_0357/06_2025/6n7i_0357_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7i_0357/06_2025/6n7i_0357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n7i_0357/06_2025/6n7i_0357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7i_0357/06_2025/6n7i_0357.map" model { file = "/net/cci-nas-00/data/ceres_data/6n7i_0357/06_2025/6n7i_0357_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7i_0357/06_2025/6n7i_0357_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 27 5.49 5 Mg 4 5.21 5 S 65 5.16 5 C 6701 2.51 5 N 1899 2.21 5 O 2137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10833 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2093 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2111 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 4, 'TRANS': 269} Chain breaks: 3 Chain: "C" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2127 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 4, 'TRANS': 271} Chain breaks: 3 Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2086 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 266} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1861 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 236} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 134 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "T" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.77, per 1000 atoms: 0.62 Number of scatterers: 10833 At special positions: 0 Unit cell: (80.25, 120.91, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 65 16.00 P 27 15.00 Mg 4 11.99 O 2137 8.00 N 1899 7.00 C 6701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 5 sheets defined 38.6% alpha, 15.3% beta 0 base pairs and 11 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 273 through 280 removed outlier: 3.687A pdb=" N SER A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 removed outlier: 4.495A pdb=" N ASN A 296 " --> pdb=" O CYS A 292 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 298 " --> pdb=" O GLY A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 298' Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.807A pdb=" N PHE A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 removed outlier: 3.785A pdb=" N THR A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 4.121A pdb=" N GLN A 364 " --> pdb=" O ARG A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 364' Processing helix chain 'A' and resid 365 through 375 removed outlier: 3.898A pdb=" N ILE A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 386 removed outlier: 3.529A pdb=" N PHE A 382 " --> pdb=" O PHE A 378 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.583A pdb=" N TYR A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 removed outlier: 4.356A pdb=" N VAL A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.574A pdb=" N ASP A 485 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 486 " --> pdb=" O ILE A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 486' Processing helix chain 'B' and resid 271 through 280 removed outlier: 3.575A pdb=" N GLU B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 removed outlier: 4.460A pdb=" N ASN B 296 " --> pdb=" O CYS B 292 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS B 298 " --> pdb=" O GLY B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 298' Processing helix chain 'B' and resid 317 through 332 removed outlier: 3.533A pdb=" N ALA B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.881A pdb=" N THR B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 373 removed outlier: 3.539A pdb=" N LYS B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 387 removed outlier: 3.764A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 415 removed outlier: 3.523A pdb=" N ALA B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.639A pdb=" N GLY B 478 " --> pdb=" O HIS B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.976A pdb=" N LEU B 486 " --> pdb=" O ILE B 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 292 through 300 removed outlier: 4.376A pdb=" N ASN C 296 " --> pdb=" O CYS C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 332 removed outlier: 3.671A pdb=" N GLN C 328 " --> pdb=" O GLN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.583A pdb=" N ALA C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.700A pdb=" N GLY C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 375 removed outlier: 3.739A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 386 removed outlier: 4.068A pdb=" N GLN C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 415 removed outlier: 3.988A pdb=" N LEU C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.606A pdb=" N VAL C 430 " --> pdb=" O ILE C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 457 removed outlier: 3.767A pdb=" N MET C 441 " --> pdb=" O ASP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 removed outlier: 4.113A pdb=" N GLY C 478 " --> pdb=" O HIS C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 3.760A pdb=" N ASP C 485 " --> pdb=" O SER C 482 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 486 " --> pdb=" O ILE C 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 482 through 486' Processing helix chain 'C' and resid 490 through 495 removed outlier: 3.635A pdb=" N GLN C 494 " --> pdb=" O GLY C 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 318 through 331 removed outlier: 3.649A pdb=" N GLN D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 removed outlier: 3.567A pdb=" N THR D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 removed outlier: 3.639A pdb=" N LYS D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG D 370 " --> pdb=" O ASP D 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 370' Processing helix chain 'D' and resid 370 through 376 removed outlier: 3.785A pdb=" N GLU D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 376 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 removed outlier: 3.559A pdb=" N ASP D 383 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 417 Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 440 through 457 removed outlier: 3.544A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 478 removed outlier: 3.832A pdb=" N GLY D 478 " --> pdb=" O HIS D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 328 Processing helix chain 'E' and resid 347 through 358 removed outlier: 3.763A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 372 removed outlier: 3.544A pdb=" N LYS E 369 " --> pdb=" O SER E 365 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 386 removed outlier: 3.663A pdb=" N GLU E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 414 Processing helix chain 'E' and resid 440 through 457 removed outlier: 3.836A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 478 Processing helix chain 'F' and resid 273 through 280 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.743A pdb=" N ILE B 463 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU B 306 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL B 462 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE B 308 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N CYS B 464 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 310 " --> pdb=" O CYS B 464 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 307 " --> pdb=" O THR B 498 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE B 500 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET B 309 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU B 502 " --> pdb=" O MET B 309 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR B 311 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 542 through 544 removed outlier: 7.050A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 307 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE A 500 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET A 309 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU A 502 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR A 311 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ARG A 504 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 421 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE A 463 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A 423 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 267 removed outlier: 6.622A pdb=" N VAL C 337 " --> pdb=" O HIS C 392 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N TYR C 394 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 339 " --> pdb=" O TYR C 394 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE C 308 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL C 307 " --> pdb=" O THR C 498 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE C 500 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N MET C 309 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU C 502 " --> pdb=" O MET C 309 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR C 311 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 516 " --> pdb=" O GLY C 531 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY C 531 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE C 518 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE C 529 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 265 through 267 removed outlier: 7.043A pdb=" N VAL E 337 " --> pdb=" O HIS E 392 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N TYR E 394 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU E 339 " --> pdb=" O TYR E 394 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE E 421 " --> pdb=" O VAL E 461 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE E 463 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU E 423 " --> pdb=" O ILE E 463 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE E 308 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N CYS E 464 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL E 310 " --> pdb=" O CYS E 464 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL E 307 " --> pdb=" O THR E 498 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ILE E 500 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET E 309 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU E 502 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR E 311 " --> pdb=" O LEU E 502 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE E 499 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR E 532 " --> pdb=" O SER E 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 391 through 392 removed outlier: 6.466A pdb=" N VAL D 337 " --> pdb=" O HIS D 392 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE D 421 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE D 463 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU D 423 " --> pdb=" O ILE D 463 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU D 306 " --> pdb=" O LEU D 460 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL D 462 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE D 308 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N CYS D 464 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL D 310 " --> pdb=" O CYS D 464 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 498 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 11 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1810 1.31 - 1.43: 2714 1.43 - 1.56: 6301 1.56 - 1.69: 49 1.69 - 1.81: 110 Bond restraints: 10984 Sorted by residual: bond pdb=" C6 TTP B 700 " pdb=" N1 TTP B 700 " ideal model delta sigma weight residual 1.337 1.430 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C6 TTP C 700 " pdb=" N1 TTP C 700 " ideal model delta sigma weight residual 1.337 1.429 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C6 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.337 1.428 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C6 TTP D 700 " pdb=" N1 TTP D 700 " ideal model delta sigma weight residual 1.337 1.428 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C2 TTP E 700 " pdb=" N1 TTP E 700 " ideal model delta sigma weight residual 1.410 1.485 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 10979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 14531 2.64 - 5.27: 234 5.27 - 7.91: 43 7.91 - 10.55: 11 10.55 - 13.19: 6 Bond angle restraints: 14825 Sorted by residual: angle pdb=" N LYS D 318 " pdb=" CA LYS D 318 " pdb=" C LYS D 318 " ideal model delta sigma weight residual 112.68 103.19 9.49 1.33e+00 5.65e-01 5.09e+01 angle pdb=" C LEU A 288 " pdb=" CA LEU A 288 " pdb=" CB LEU A 288 " ideal model delta sigma weight residual 109.84 101.69 8.15 1.63e+00 3.76e-01 2.50e+01 angle pdb=" PA TTP D 700 " pdb=" O3A TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sigma weight residual 120.50 133.69 -13.19 3.00e+00 1.11e-01 1.93e+01 angle pdb=" PA TTP B 700 " pdb=" O3A TTP B 700 " pdb=" PB TTP B 700 " ideal model delta sigma weight residual 120.50 133.20 -12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" PA TTP E 700 " pdb=" O3A TTP E 700 " pdb=" PB TTP E 700 " ideal model delta sigma weight residual 120.50 132.39 -11.89 3.00e+00 1.11e-01 1.57e+01 ... (remaining 14820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 6410 35.51 - 71.03: 125 71.03 - 106.54: 10 106.54 - 142.06: 3 142.06 - 177.57: 6 Dihedral angle restraints: 6554 sinusoidal: 2795 harmonic: 3759 Sorted by residual: dihedral pdb=" O2G TTP D 700 " pdb=" O3B TTP D 700 " pdb=" PG TTP D 700 " pdb=" PB TTP D 700 " ideal model delta sinusoidal sigma weight residual -180.00 -2.43 -177.57 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2G TTP E 700 " pdb=" O3B TTP E 700 " pdb=" PG TTP E 700 " pdb=" PB TTP E 700 " ideal model delta sinusoidal sigma weight residual -180.00 -6.25 -173.75 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C2 TTP C 700 " pdb=" C1' TTP C 700 " pdb=" N1 TTP C 700 " pdb=" O4' TTP C 700 " ideal model delta sinusoidal sigma weight residual -58.32 101.51 -159.82 1 2.00e+01 2.50e-03 4.65e+01 ... (remaining 6551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1401 0.071 - 0.142: 260 0.142 - 0.214: 22 0.214 - 0.285: 4 0.285 - 0.356: 1 Chirality restraints: 1688 Sorted by residual: chirality pdb=" CA ASN B 388 " pdb=" N ASN B 388 " pdb=" C ASN B 388 " pdb=" CB ASN B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C3' TTP E 700 " pdb=" C2' TTP E 700 " pdb=" C4' TTP E 700 " pdb=" O3' TTP E 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C3' TTP D 700 " pdb=" C2' TTP D 700 " pdb=" C4' TTP D 700 " pdb=" O3' TTP D 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1685 not shown) Planarity restraints: 1822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 413 " 0.918 9.50e-02 1.11e+02 4.12e-01 1.03e+02 pdb=" NE ARG D 413 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG D 413 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 413 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 413 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 504 " 0.828 9.50e-02 1.11e+02 3.71e-01 8.37e+01 pdb=" NE ARG A 504 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG A 504 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 504 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 504 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 276 " -0.736 9.50e-02 1.11e+02 3.30e-01 6.63e+01 pdb=" NE ARG A 276 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG A 276 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 276 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 276 " -0.022 2.00e-02 2.50e+03 ... (remaining 1819 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 252 2.71 - 3.25: 9516 3.25 - 3.80: 16307 3.80 - 4.35: 21738 4.35 - 4.90: 36488 Nonbonded interactions: 84301 Sorted by model distance: nonbonded pdb=" NE2 GLN C 343 " pdb="MG MG C 701 " model vdw 2.157 2.250 nonbonded pdb=" O1B TTP B 700 " pdb="MG MG B 701 " model vdw 2.185 2.170 nonbonded pdb=" O1G TTP B 700 " pdb="MG MG B 701 " model vdw 2.200 2.170 nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.223 2.170 nonbonded pdb=" O2B TTP E 700 " pdb="MG MG E 701 " model vdw 2.223 2.170 ... (remaining 84296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 506 or resid 510 through 545)) selection = (chain 'B' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 506 or resid 510 through 545)) selection = (chain 'C' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 545)) selection = (chain 'D' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 through 506 or resid 510 through 545)) selection = (chain 'E' and (resid 285 through 506 or resid 510 through 545)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.950 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 10984 Z= 0.300 Angle : 0.911 13.186 14825 Z= 0.488 Chirality : 0.055 0.356 1688 Planarity : 0.017 0.412 1822 Dihedral : 14.815 177.571 4148 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.53 % Allowed : 4.58 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.19), residues: 1308 helix: -2.86 (0.17), residues: 432 sheet: -0.33 (0.35), residues: 254 loop : -2.71 (0.20), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 381 HIS 0.009 0.001 HIS B 425 PHE 0.011 0.002 PHE D 523 TYR 0.007 0.001 TYR A 547 ARG 0.007 0.001 ARG B 479 Details of bonding type rmsd hydrogen bonds : bond 0.15509 ( 350) hydrogen bonds : angle 7.84658 ( 1008) covalent geometry : bond 0.00527 (10984) covalent geometry : angle 0.91098 (14825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 319 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 341 MET cc_start: 0.7360 (mmt) cc_final: 0.7118 (mmt) REVERT: A 513 LEU cc_start: 0.7069 (tp) cc_final: 0.6772 (tp) REVERT: B 408 LYS cc_start: 0.7905 (mttp) cc_final: 0.7683 (mmmt) REVERT: E 470 ASP cc_start: 0.5859 (p0) cc_final: 0.5578 (m-30) REVERT: E 532 TYR cc_start: 0.7350 (m-80) cc_final: 0.7149 (m-80) outliers start: 6 outliers final: 0 residues processed: 321 average time/residue: 0.3011 time to fit residues: 127.2100 Evaluate side-chains 145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 121 optimal weight: 0.0870 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 465 HIS A 512 ASN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS D 325 GLN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.164943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140145 restraints weight = 14281.139| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.66 r_work: 0.3707 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10984 Z= 0.172 Angle : 0.630 9.175 14825 Z= 0.309 Chirality : 0.044 0.153 1688 Planarity : 0.004 0.043 1822 Dihedral : 15.995 162.881 1642 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.11 % Allowed : 10.04 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.22), residues: 1308 helix: -1.03 (0.22), residues: 451 sheet: -0.11 (0.34), residues: 252 loop : -2.13 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 541 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.002 PHE D 452 TYR 0.019 0.001 TYR D 411 ARG 0.009 0.001 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 350) hydrogen bonds : angle 5.19362 ( 1008) covalent geometry : bond 0.00398 (10984) covalent geometry : angle 0.62975 (14825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: A 380 GLN cc_start: 0.6958 (mt0) cc_final: 0.6620 (mt0) REVERT: B 273 GLU cc_start: 0.8370 (tp30) cc_final: 0.8098 (mp0) REVERT: B 359 ARG cc_start: 0.8219 (mpt180) cc_final: 0.7864 (mmt90) REVERT: B 408 LYS cc_start: 0.8110 (mttp) cc_final: 0.7709 (mmmt) REVERT: E 316 MET cc_start: 0.8163 (mmm) cc_final: 0.7840 (mmt) REVERT: E 470 ASP cc_start: 0.6123 (p0) cc_final: 0.5854 (m-30) REVERT: E 532 TYR cc_start: 0.7411 (m-80) cc_final: 0.7188 (m-80) outliers start: 24 outliers final: 15 residues processed: 174 average time/residue: 0.2518 time to fit residues: 60.3568 Evaluate side-chains 147 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 482 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 62 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS B 357 HIS B 507 GLN C 324 GLN C 358 ASN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.158589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.134819 restraints weight = 14753.634| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.62 r_work: 0.3636 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10984 Z= 0.241 Angle : 0.699 9.257 14825 Z= 0.344 Chirality : 0.047 0.178 1688 Planarity : 0.004 0.046 1822 Dihedral : 15.975 160.458 1642 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.79 % Allowed : 11.19 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.22), residues: 1308 helix: -0.59 (0.23), residues: 453 sheet: -0.30 (0.33), residues: 254 loop : -1.86 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 381 HIS 0.009 0.002 HIS D 475 PHE 0.027 0.003 PHE E 523 TYR 0.016 0.001 TYR D 411 ARG 0.017 0.001 ARG E 363 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 350) hydrogen bonds : angle 5.05014 ( 1008) covalent geometry : bond 0.00580 (10984) covalent geometry : angle 0.69908 (14825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7264 (mpp) REVERT: A 380 GLN cc_start: 0.6949 (mt0) cc_final: 0.6656 (mt0) REVERT: B 408 LYS cc_start: 0.7975 (mttp) cc_final: 0.7665 (mmmt) REVERT: B 487 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7939 (ttt90) outliers start: 43 outliers final: 31 residues processed: 170 average time/residue: 0.2418 time to fit residues: 59.0140 Evaluate side-chains 149 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 503 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 121 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 66 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.159672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135096 restraints weight = 14466.738| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.71 r_work: 0.3634 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10984 Z= 0.107 Angle : 0.539 8.014 14825 Z= 0.267 Chirality : 0.042 0.152 1688 Planarity : 0.003 0.041 1822 Dihedral : 15.393 158.897 1642 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.20 % Allowed : 13.83 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1308 helix: 0.00 (0.24), residues: 453 sheet: -0.01 (0.34), residues: 256 loop : -1.62 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 381 HIS 0.006 0.001 HIS B 425 PHE 0.012 0.001 PHE C 321 TYR 0.015 0.001 TYR D 411 ARG 0.004 0.000 ARG F 276 Details of bonding type rmsd hydrogen bonds : bond 0.02811 ( 350) hydrogen bonds : angle 4.54894 ( 1008) covalent geometry : bond 0.00248 (10984) covalent geometry : angle 0.53878 (14825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.164 Fit side-chains REVERT: A 316 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7505 (mpp) REVERT: B 408 LYS cc_start: 0.7872 (mttp) cc_final: 0.7534 (mmmt) REVERT: B 428 ILE cc_start: 0.7442 (mt) cc_final: 0.7192 (mt) REVERT: D 319 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8188 (m) REVERT: D 341 MET cc_start: 0.7860 (mmt) cc_final: 0.7565 (mmp) REVERT: D 452 PHE cc_start: 0.8679 (t80) cc_final: 0.8450 (t80) REVERT: E 510 MET cc_start: 0.7253 (ptp) cc_final: 0.6742 (mtp) REVERT: F 274 ARG cc_start: 0.6140 (mtp180) cc_final: 0.5210 (mtp180) outliers start: 25 outliers final: 16 residues processed: 159 average time/residue: 0.2604 time to fit residues: 58.4907 Evaluate side-chains 144 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 503 GLU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 482 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 50 optimal weight: 0.0770 chunk 114 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS A 444 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130586 restraints weight = 14627.461| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.73 r_work: 0.3578 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10984 Z= 0.181 Angle : 0.608 8.907 14825 Z= 0.300 Chirality : 0.044 0.146 1688 Planarity : 0.003 0.040 1822 Dihedral : 15.591 160.471 1642 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.44 % Allowed : 13.74 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.23), residues: 1308 helix: 0.14 (0.24), residues: 447 sheet: 0.04 (0.34), residues: 251 loop : -1.47 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 329 HIS 0.006 0.001 HIS D 475 PHE 0.016 0.002 PHE C 321 TYR 0.015 0.001 TYR D 411 ARG 0.006 0.001 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 350) hydrogen bonds : angle 4.62571 ( 1008) covalent geometry : bond 0.00433 (10984) covalent geometry : angle 0.60778 (14825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 2.028 Fit side-chains REVERT: A 316 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7190 (mpp) REVERT: A 386 PHE cc_start: 0.6762 (m-80) cc_final: 0.6490 (t80) REVERT: A 460 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7748 (tt) REVERT: B 408 LYS cc_start: 0.7903 (mttp) cc_final: 0.7582 (mmmt) REVERT: B 428 ILE cc_start: 0.7621 (mt) cc_final: 0.7301 (mt) REVERT: D 319 SER cc_start: 0.8508 (OUTLIER) cc_final: 0.8296 (m) REVERT: D 452 PHE cc_start: 0.8681 (t80) cc_final: 0.8425 (t80) REVERT: D 518 ILE cc_start: 0.9071 (mm) cc_final: 0.8830 (mm) REVERT: E 446 MET cc_start: 0.6530 (mmt) cc_final: 0.5716 (mmt) outliers start: 39 outliers final: 30 residues processed: 150 average time/residue: 0.2502 time to fit residues: 55.1357 Evaluate side-chains 152 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 503 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain E residue 516 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.0170 chunk 52 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 112 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN D 468 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.163951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140490 restraints weight = 14534.557| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.63 r_work: 0.3710 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10984 Z= 0.098 Angle : 0.518 8.215 14825 Z= 0.258 Chirality : 0.042 0.152 1688 Planarity : 0.002 0.039 1822 Dihedral : 15.146 158.323 1642 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.73 % Allowed : 15.15 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1308 helix: 0.52 (0.25), residues: 455 sheet: 0.14 (0.34), residues: 256 loop : -1.31 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 381 HIS 0.004 0.001 HIS C 425 PHE 0.012 0.001 PHE C 321 TYR 0.014 0.001 TYR D 411 ARG 0.007 0.000 ARG F 276 Details of bonding type rmsd hydrogen bonds : bond 0.02675 ( 350) hydrogen bonds : angle 4.33388 ( 1008) covalent geometry : bond 0.00220 (10984) covalent geometry : angle 0.51833 (14825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 1.254 Fit side-chains REVERT: A 316 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7569 (mpp) REVERT: A 460 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7682 (tt) REVERT: B 408 LYS cc_start: 0.7788 (mttp) cc_final: 0.7550 (mmmt) REVERT: B 428 ILE cc_start: 0.7552 (mt) cc_final: 0.7254 (mt) REVERT: D 375 ASN cc_start: 0.7465 (OUTLIER) cc_final: 0.7231 (t0) REVERT: E 446 MET cc_start: 0.6531 (mmt) cc_final: 0.5537 (mmt) REVERT: E 510 MET cc_start: 0.7273 (ptp) cc_final: 0.6895 (mtp) outliers start: 31 outliers final: 24 residues processed: 158 average time/residue: 0.2284 time to fit residues: 52.3326 Evaluate side-chains 146 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 503 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 20 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 122 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 0.0030 chunk 95 optimal weight: 4.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN C 324 GLN ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN D 468 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.164320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140755 restraints weight = 14616.434| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.64 r_work: 0.3718 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10984 Z= 0.099 Angle : 0.532 10.971 14825 Z= 0.261 Chirality : 0.042 0.147 1688 Planarity : 0.002 0.039 1822 Dihedral : 14.934 159.069 1642 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.00 % Allowed : 15.33 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1308 helix: 0.82 (0.25), residues: 445 sheet: 0.24 (0.34), residues: 265 loop : -1.24 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 381 HIS 0.004 0.001 HIS C 425 PHE 0.013 0.001 PHE C 321 TYR 0.009 0.001 TYR A 394 ARG 0.008 0.000 ARG F 276 Details of bonding type rmsd hydrogen bonds : bond 0.02633 ( 350) hydrogen bonds : angle 4.25423 ( 1008) covalent geometry : bond 0.00226 (10984) covalent geometry : angle 0.53185 (14825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.148 Fit side-chains REVERT: A 316 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7476 (mpp) REVERT: A 388 ASN cc_start: 0.6899 (m-40) cc_final: 0.6319 (t0) REVERT: A 460 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7691 (tt) REVERT: B 408 LYS cc_start: 0.7748 (mttp) cc_final: 0.7497 (mmmt) REVERT: E 446 MET cc_start: 0.6545 (mmt) cc_final: 0.5502 (mmt) REVERT: E 510 MET cc_start: 0.7244 (ptp) cc_final: 0.6772 (mtp) outliers start: 34 outliers final: 23 residues processed: 153 average time/residue: 0.2041 time to fit residues: 46.2045 Evaluate side-chains 150 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 503 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 81 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.160344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136816 restraints weight = 14603.586| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.62 r_work: 0.3664 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10984 Z= 0.154 Angle : 0.587 10.324 14825 Z= 0.288 Chirality : 0.043 0.146 1688 Planarity : 0.003 0.037 1822 Dihedral : 15.153 159.496 1642 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.00 % Allowed : 15.51 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1308 helix: 0.75 (0.25), residues: 443 sheet: 0.21 (0.33), residues: 260 loop : -1.19 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 381 HIS 0.005 0.001 HIS D 475 PHE 0.016 0.002 PHE C 321 TYR 0.014 0.001 TYR D 411 ARG 0.008 0.000 ARG F 276 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 350) hydrogen bonds : angle 4.39642 ( 1008) covalent geometry : bond 0.00367 (10984) covalent geometry : angle 0.58658 (14825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.134 Fit side-chains REVERT: A 316 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7363 (mpp) REVERT: A 388 ASN cc_start: 0.6932 (m-40) cc_final: 0.6320 (t0) REVERT: A 460 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7725 (tt) REVERT: B 408 LYS cc_start: 0.7829 (mttp) cc_final: 0.7594 (mmmt) REVERT: B 428 ILE cc_start: 0.7441 (mt) cc_final: 0.7107 (mt) REVERT: E 316 MET cc_start: 0.8125 (mmm) cc_final: 0.7839 (mmm) REVERT: E 446 MET cc_start: 0.6658 (mmt) cc_final: 0.5753 (mmt) REVERT: E 510 MET cc_start: 0.7325 (ptp) cc_final: 0.6962 (mtp) outliers start: 34 outliers final: 30 residues processed: 148 average time/residue: 0.2080 time to fit residues: 44.9713 Evaluate side-chains 151 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 503 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 81 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.158653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135098 restraints weight = 14768.071| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.63 r_work: 0.3645 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10984 Z= 0.181 Angle : 0.625 10.304 14825 Z= 0.305 Chirality : 0.045 0.146 1688 Planarity : 0.003 0.035 1822 Dihedral : 15.301 159.551 1642 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.70 % Allowed : 14.71 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.24), residues: 1308 helix: 0.65 (0.25), residues: 443 sheet: 0.08 (0.33), residues: 261 loop : -1.21 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 381 HIS 0.005 0.001 HIS D 475 PHE 0.016 0.002 PHE C 321 TYR 0.015 0.001 TYR D 411 ARG 0.007 0.001 ARG F 276 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 350) hydrogen bonds : angle 4.50517 ( 1008) covalent geometry : bond 0.00434 (10984) covalent geometry : angle 0.62536 (14825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 1.263 Fit side-chains REVERT: A 316 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7380 (mpp) REVERT: A 388 ASN cc_start: 0.7021 (m-40) cc_final: 0.6442 (t0) REVERT: A 460 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7774 (tt) REVERT: B 408 LYS cc_start: 0.7902 (mttp) cc_final: 0.7649 (mmmt) REVERT: B 428 ILE cc_start: 0.7484 (mt) cc_final: 0.7125 (mt) REVERT: D 319 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8299 (m) REVERT: D 518 ILE cc_start: 0.9137 (mm) cc_final: 0.8870 (mm) REVERT: E 385 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6861 (tp) REVERT: E 446 MET cc_start: 0.6575 (mmt) cc_final: 0.5678 (mmt) REVERT: E 510 MET cc_start: 0.7206 (ptp) cc_final: 0.6725 (mtp) outliers start: 42 outliers final: 37 residues processed: 147 average time/residue: 0.2163 time to fit residues: 46.5398 Evaluate side-chains 157 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 503 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 516 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 36 optimal weight: 4.9990 chunk 37 optimal weight: 0.0670 chunk 130 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN D 468 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.162175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.138696 restraints weight = 14541.052| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.63 r_work: 0.3690 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10984 Z= 0.111 Angle : 0.548 11.078 14825 Z= 0.271 Chirality : 0.042 0.147 1688 Planarity : 0.002 0.038 1822 Dihedral : 14.963 158.236 1642 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.00 % Allowed : 15.42 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1308 helix: 0.85 (0.26), residues: 443 sheet: 0.27 (0.33), residues: 263 loop : -1.17 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 381 HIS 0.004 0.001 HIS C 425 PHE 0.014 0.001 PHE C 321 TYR 0.014 0.001 TYR D 411 ARG 0.007 0.000 ARG F 276 Details of bonding type rmsd hydrogen bonds : bond 0.02773 ( 350) hydrogen bonds : angle 4.33887 ( 1008) covalent geometry : bond 0.00260 (10984) covalent geometry : angle 0.54835 (14825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 1.296 Fit side-chains REVERT: A 316 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7673 (mpp) REVERT: A 388 ASN cc_start: 0.6984 (m-40) cc_final: 0.6466 (t0) REVERT: A 460 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7703 (tt) REVERT: B 408 LYS cc_start: 0.7809 (mttp) cc_final: 0.7601 (mmmt) REVERT: B 428 ILE cc_start: 0.7366 (mt) cc_final: 0.7040 (mt) REVERT: D 375 ASN cc_start: 0.7348 (OUTLIER) cc_final: 0.7125 (t0) REVERT: D 518 ILE cc_start: 0.9029 (mm) cc_final: 0.8802 (mm) REVERT: E 316 MET cc_start: 0.8103 (mmm) cc_final: 0.7794 (mmm) REVERT: E 446 MET cc_start: 0.6504 (mmt) cc_final: 0.5573 (mmt) REVERT: E 510 MET cc_start: 0.7213 (ptp) cc_final: 0.6877 (mtp) outliers start: 34 outliers final: 26 residues processed: 145 average time/residue: 0.2640 time to fit residues: 55.3471 Evaluate side-chains 146 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 473 LYS Chi-restraints excluded: chain C residue 503 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 375 ASN Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain E residue 290 SER Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 477 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 130 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 119 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.157479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.134004 restraints weight = 14618.283| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.61 r_work: 0.3629 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10984 Z= 0.215 Angle : 0.661 10.706 14825 Z= 0.323 Chirality : 0.046 0.149 1688 Planarity : 0.003 0.038 1822 Dihedral : 15.401 160.025 1642 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.35 % Allowed : 15.07 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1308 helix: 0.61 (0.25), residues: 443 sheet: 0.12 (0.33), residues: 258 loop : -1.19 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 329 HIS 0.007 0.001 HIS D 475 PHE 0.017 0.002 PHE C 321 TYR 0.013 0.001 TYR D 411 ARG 0.009 0.001 ARG F 276 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 350) hydrogen bonds : angle 4.60601 ( 1008) covalent geometry : bond 0.00515 (10984) covalent geometry : angle 0.66102 (14825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6038.16 seconds wall clock time: 104 minutes 57.13 seconds (6297.13 seconds total)